Aligning sequencing reads onto a reference is an essential step of the majority of genomic
analysis pipelines. Computational algorithms for read alignment have evolved in …

Gene expression is the fundamental level at which the results of various genetic and
regulatory programs are observable. The measurement of transcriptome-wide gene …

Since the first half of the twentieth century, evolutionary theory has been dominated by the
idea that mutations occur randomly with respect to their consequences. Here we test this …

We report the first annotated chromosome-level reference genome assembly for pea, Gregor
Mendel's original genetic model. Phylogenetics and paleogenomics show genomic …

We present RaGOO, a reference-guided contig ordering and orienting tool that leverages
the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies …

Sequencing technologies using nucleotide conversion techniques such as cytosine to
thymine in bisulfite-seq and thymine to cytosine in SLAM seq are powerful tools to explore …

The biological and functional heterogeneity between tumors—both across and within cancer
types—poses a challenge for immunotherapy. To understand the factors underlying tumor …

Structural variations are the greatest source of genetic variation, but they remain poorly
understood because of technological limitations. Single-molecule long-read sequencing has …

Species often include multiple ecotypes that are adapted to different environments.
However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive …

Gene expression profiling by high-throughput sequencing reveals qualitative and
quantitative changes in RNA species at steady state but obscures the intracellular dynamics …